Tue Nov 22 14:12:49 PST 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:12:51 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6422515 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -4.220000 35.05000 ymin,ymax (A): -4.441000 48.56500 zmin,zma (A): -24.10200 31.32800 x,y,z range (A): 39.27000 53.00600 55.43000 scale (grids/A): 0.6422515 object centre (A): 15.41500 22.06200 3.613000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 290.6260 centred at (gu) : 90.27424 92.90518 90.02437 assigned negative charge : -285.6263 centred at (gu) : 90.31507 92.98309 89.97428 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5599 nv = 96 ne = 84 npr = 40165 no. pairs analyzed = 40165 no. exposed pairs = 2413 no. arc points = 17019 no. surface atoms = 823 nbur = 1139 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3183 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2000000 number of dielectric boundary points 2696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1647 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 6468 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3713885E-09 1.2499783E-08 midg,1,midg; midg,igrid,midg 8.1561815E-09 1.0816481E-09 1,midg,midg; igrid,midg,midg 1.0960701E-08 4.4653738E-09 gauss-seidel spectral radius is 0.9873835 estimated iterations to convergence 73 setup time was (sec) 0.4300000 now iterating at: 14:12:54 rms-change max change #iterations 0.1265098 18.56700 at 10iterations 1.2742308E-02 1.770814 at 20iterations 1.2604865E-03 0.2046585 at 30iterations 1.2778898E-04 1.9058228E-02 at 40iterations 1.2341489E-05 1.9683838E-03 at 50iterations finished qdiffx linear iterations at : 14:13:03 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 1.2341489E-05 1.9683838E-03 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 14:13:06 3.201u 0.168s 0:15.83 21.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:13:08 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.926754 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -4.220000 35.05000 ymin,ymax (A): -4.441000 48.56500 zmin,zma (A): -24.10200 31.32800 x,y,z range (A): 39.27000 53.00600 55.43000 scale (grids/A): 1.926754 object centre (A): 15.41500 22.06200 3.613000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 290.6260 centred at (gu) : 90.82244 98.71537 90.07321 assigned negative charge : -285.6263 centred at (gu) : 90.94550 98.94940 89.92294 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 59709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17019 grid for indexing accessible points = 1.400000 m= 22423 mr = 41473 m= 3408 mr = 17294 m= 143 mr = 2240 m= 0 mr = 34 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2499 time to turn everything in is 0.4100000 number of dielectric boundary points 24642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14423 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6422515 object centre at (A) : 15.41500 22.06200 3.613000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0616812E-02 2.3535596E-02 midg,1,midg; midg,igrid,midg 3.3259206E-02 7.6183379E-03 1,midg,midg; igrid,midg,midg 4.1247914E-03 1.4760674E-04 gauss-seidel spectral radius is 0.9985865 estimated iterations to convergence 211 setup time was (sec) 0.6600000 now iterating at: 14:13:13 rms-change max change #iterations 3.662241 160.0754 at 10iterations 1.690770 71.99796 at 20iterations 0.7811859 32.51173 at 30iterations 0.3626956 13.22422 at 40iterations 0.1672430 5.785239 at 50iterations 7.7255756E-02 2.668568 at 60iterations 3.5608616E-02 1.262159 at 70iterations 1.6516164E-02 0.6094551 at 80iterations 7.5900569E-03 0.3155832 at 90iterations 3.5175490E-03 0.1300015 at 100iterations 1.6211758E-03 5.2039146E-02 at 110iterations 7.5149752E-04 2.4425507E-02 at 120iterations finished qdiffx linear iterations at : 14:13:31 total time elapsed so far: 6.690000 # loops : 120 mean,max change (kT/e) : 7.5149752E-04 2.4425507E-02 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 14:13:35 6.863u 0.174s 0:27.66 25.4% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Nov 22 2011 at 14:13:37 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.890132 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -4.220000 35.05000 ymin,ymax (A): -4.441000 48.56500 zmin,zma (A): -24.10200 31.32800 x,y,z range (A): 39.27000 53.00600 55.43000 scale (grids/A): 2.890132 object centre (A): 15.41500 22.06200 3.613000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 290.6260 centred at (gu) : 91.23372 103.0732 90.10973 assigned negative charge : -285.6263 centred at (gu) : 91.41824 103.4242 89.88432 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 137806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17019 grid for indexing accessible points = 1.400000 m= 71489 mr = 100001 m= 26951 mr = 59719 m= 6108 mr = 22479 m= 651 mr = 4764 m= 26 mr = 438 m= 0 mr = 6 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 8333 time to turn everything in is 1.020000 number of dielectric boundary points 55624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 14640 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.926754 object centre at (A) : 15.41500 22.06200 3.613000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.131388 7.7584721E-02 midg,1,midg; midg,igrid,midg 0.3336018 -1.6782334E-02 1,midg,midg; igrid,midg,midg 2.3112087E-02 2.5339771E-04 gauss-seidel spectral radius is 0.9992331 estimated iterations to convergence 285 setup time was (sec) 1.300000 now iterating at: 14:13:45 rms-change max change #iterations 8.578761 443.0720 at 10iterations 4.929718 116.7169 at 20iterations 2.804765 71.54304 at 30iterations 1.593325 31.69897 at 40iterations 0.9079068 16.80822 at 50iterations 0.5160108 10.78328 at 60iterations 0.2922685 5.922684 at 70iterations 0.1664367 3.427894 at 80iterations 9.4214328E-02 1.816654 at 90iterations 5.3480066E-02 1.101960 at 100iterations 3.0385662E-02 0.5832148 at 110iterations 1.7242003E-02 0.3702698 at 120iterations 9.7774938E-03 0.1884975 at 130iterations 5.5475975E-03 0.1120071 at 140iterations 3.1527700E-03 6.3319206E-02 at 150iterations 1.7889926E-03 3.6231995E-02 at 160iterations 1.0158604E-03 2.1671027E-02 at 170iterations 5.7646754E-04 1.2844086E-02 at 180iterations finished qdiffx linear iterations at : 14:14:12 total time elapsed so far: 11.22000 # loops : 180 mean,max change (kT/e) : 5.7646754E-04 1.2844086E-02 energy calculations done at 11.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.40000 DelPhi exited at 14:14:16 11.401u 0.154s 0:39.91 28.9% 0+0k 0+0io 0pf+0w